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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Pseudomonas putida (strain KT2440)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalytic activityi

ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide.UniRule annotation

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 1 Mg(2+) or Mn2+ ion per subunit.By similarity

Pathway: IMP biosynthesis via de novo pathway

This protein is involved in step 2 of the subpathway that synthesizes N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-alpha-D-ribose 1-diphosphate.UniRule annotation
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Amidophosphoribosyltransferase (purF)
  2. Phosphoribosylamine--glycine ligase (purD)
This subpathway is part of the pathway IMP biosynthesis via de novo pathway, which is itself part of Purine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-alpha-D-ribose 1-diphosphate, the pathway IMP biosynthesis via de novo pathway and in Purine metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi285 – 2851Magnesium or manganeseUniRule annotation
Metal bindingi287 – 2871Magnesium or manganeseUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi134 – 19562ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Purine biosynthesis

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciPPUT160488:GIXO-4917-MONOMER.
UniPathwayiUPA00074; UER00125.

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphoribosylamine--glycine ligaseUniRule annotation (EC:6.3.4.13UniRule annotation)
Alternative name(s):
GARSUniRule annotation
Glycinamide ribonucleotide synthetaseUniRule annotation
Phosphoribosylglycinamide synthetaseUniRule annotation
Gene namesi
Name:purDUniRule annotation
Ordered Locus Names:PP_4823
OrganismiPseudomonas putida (strain KT2440)
Taxonomic identifieri160488 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
ProteomesiUP000000556 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 431431Phosphoribosylamine--glycine ligasePRO_0000151470Add
BLAST

Proteomic databases

PRIDEiQ88DK2.

Interactioni

Protein-protein interaction databases

STRINGi160488.PP_4823.

Structurei

3D structure databases

ProteinModelPortaliQ88DK2.
SMRiQ88DK2. Positions 1-424.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini108 – 315208ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the GARS family.UniRule annotation
Contains 1 ATP-grasp domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG0151.
HOGENOMiHOG000033463.
KOiK01945.
OMAiEPKLENV.
OrthoDBiEOG69SKD1.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
3.90.600.10. 1 hit.
HAMAPiMF_00138. GARS.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR016185. PreATP-grasp_dom.
IPR020561. PRibGlycinamid_synth_ATP-grasp.
IPR000115. PRibGlycinamide_synth.
IPR020560. PRibGlycinamide_synth_C-dom.
IPR020559. PRibGlycinamide_synth_CS.
IPR020562. PRibGlycinamide_synth_N.
IPR011054. Rudment_hybrid_motif.
[Graphical view]
PfamiPF01071. GARS_A. 1 hit.
PF02843. GARS_C. 1 hit.
PF02844. GARS_N. 1 hit.
[Graphical view]
SUPFAMiSSF51246. SSF51246. 1 hit.
SSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR00877. purD. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00184. GARS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q88DK2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKVLIIGSGG REHALAWKVA QDPRVEKVFV APGNAGTAIE AKCENVAIDV
60 70 80 90 100
CALEQLADFA EKNVDLTIVG PEAPLVIGVV DLFRSRGLDC FGPTKGAAQL
110 120 130 140 150
EGSKAFTKDF LARHEIPTAD YQNFTEIEPA LAYLQEKGAP IVIKADGLAA
160 170 180 190 200
GKGVIVAMTL EEAEAAVRDM LAGNAFGEAG SRVVIEEFLD GEEASFIVMV
210 220 230 240 250
DGHNVLPMAT SQDHKRVGDQ DTGPNTGGMG AYSPAPVVTA DVHQRVMDQV
260 270 280 290 300
IWPTVRGMAE EGNVYTGFLY AGLMIDKAGN PKVIEFNCRF GDPETQPVML
310 320 330 340 350
RLESSLVLLV EAAFAKALDK VEAQWDPRPS LGVVLAAGGY PGDYAKGDVI
360 370 380 390 400
NGLDAAAKIE GKVFHAGTAL KDGKVTTNGG RVLCATAMGS TVADAQQQAY
410 420 430
RLAKEVSWNG SFYRSDIGYR AIARERGEHQ Q
Length:431
Mass (Da):45,837
Last modified:June 1, 2003 - v1
Checksum:i0F55678D9CB72F51
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE015451 Genomic DNA. Translation: AAN70392.1.
RefSeqiNP_746928.1. NC_002947.3.
WP_010955432.1. NC_002947.3.

Genome annotation databases

EnsemblBacteriaiAAN70392; AAN70392; PP_4823.
GeneIDi1043159.
KEGGippu:PP_4823.
PATRICi19948432. VBIPsePut30601_5147.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE015451 Genomic DNA. Translation: AAN70392.1.
RefSeqiNP_746928.1. NC_002947.3.
WP_010955432.1. NC_002947.3.

3D structure databases

ProteinModelPortaliQ88DK2.
SMRiQ88DK2. Positions 1-424.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi160488.PP_4823.

Proteomic databases

PRIDEiQ88DK2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN70392; AAN70392; PP_4823.
GeneIDi1043159.
KEGGippu:PP_4823.
PATRICi19948432. VBIPsePut30601_5147.

Phylogenomic databases

eggNOGiCOG0151.
HOGENOMiHOG000033463.
KOiK01945.
OMAiEPKLENV.
OrthoDBiEOG69SKD1.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.
BioCyciPPUT160488:GIXO-4917-MONOMER.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
3.90.600.10. 1 hit.
HAMAPiMF_00138. GARS.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR016185. PreATP-grasp_dom.
IPR020561. PRibGlycinamid_synth_ATP-grasp.
IPR000115. PRibGlycinamide_synth.
IPR020560. PRibGlycinamide_synth_C-dom.
IPR020559. PRibGlycinamide_synth_CS.
IPR020562. PRibGlycinamide_synth_N.
IPR011054. Rudment_hybrid_motif.
[Graphical view]
PfamiPF01071. GARS_A. 1 hit.
PF02843. GARS_C. 1 hit.
PF02844. GARS_N. 1 hit.
[Graphical view]
SUPFAMiSSF51246. SSF51246. 1 hit.
SSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR00877. purD. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00184. GARS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: KT2440.

Entry informationi

Entry nameiPUR2_PSEPK
AccessioniPrimary (citable) accession number: Q88DK2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 24, 2003
Last sequence update: June 1, 2003
Last modified: May 27, 2015
This is version 84 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.